setup.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import pathlib
import re
import sys

from setuptools import setup
from setuptools.command.sdist import sdist as SdistCommand
from setuptools.command.test import test as TestCommand

# If could not build wheels for gseapy which use PEP 517
# need to pip install --upgrade pip setuptools wheel
# or conda update setuptools wheel

try:
    from setuptools_rust import Binding, RustExtension
except ImportError:
    import subprocess

    errno = subprocess.call([sys.executable, "-m", "pip", "install", "setuptools-rust"])
    if errno:
        print("Please install setuptools-rust package")
        raise SystemExit(errno)
    else:
        from setuptools_rust import Binding, RustExtension


def find_version():
    filepath = os.path.join("gseapy", "__main__.py")
    with open(os.path.join(os.path.dirname(__file__), filepath), encoding="utf8") as fp:
        content = fp.read()
    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", content, re.M)
    if version_match:
        return version_match.group(1)
    raise RuntimeError("Unable to find version string.")


__author__ = "Zhuoqing Fang"
__version__ = find_version()


class PyTest(TestCommand):
    def finalize_options(self):
        TestCommand.finalize_options(self)
        self.test_args = []
        self.test_suite = True

    def run_tests(self):
        # import here, cause outside the eggs aren't loaded
        import pytest

        errno = pytest.main(self.test_args)
        sys.exit(errno)


class CargoModifiedSdist(SdistCommand):
    def make_release_tree(self, base_dir, files):
        """Stages the files to be included in archives"""
        files.append("Cargo.toml")
        files += [str(f) for f in pathlib.Path("src").glob("**/*.rs") if f.is_file()]
        super().make_release_tree(base_dir, files)


def readme():
    with open("README.rst") as f:
        return f.read()


setup(
    name="gseapy",
    version=__version__,
    description="Gene Set Enrichment Analysis in Python",
    long_description=readme(),
    long_description_content_type="text/x-rst",
    classifiers=[
        "Development Status :: 4 - Beta",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: MIT License",
        "Programming Language :: Python :: 3",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: Microsoft :: Windows",
        "Operating System :: POSIX",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Software Development :: Libraries",
    ],
    keywords=[
        "Gene Ontology",
        "GO",
        "Biology",
        "Enrichment",
        "Bioinformatics",
        "Computational Biology",
    ],
    url="https://github.com/zqfang/gseapy",
    author=__author__,
    author_email="fzq518@gmail.com",
    license="MIT",
    packages=["gseapy"],
    package_data={
        "gseapy": ["data/palette.json"],
    },
    include_package_data=False,
    project_urls={
        "Documentation": "https://gseapy.readthedocs.io/en/latest/",
        "Source": "https://github.com/zqfang/GSEApy",
        "Tracker": "https://github.com/zqfang/GSEApy/issues",
    },
    python_requires=">=3.7",
    setup_requires=["setuptools-rust>=0.10.1", "wheel"],
    install_requires=[
        "numpy>=1.13.0",
        "scipy",
        "pandas",
        "matplotlib>=2.2",
        "requests",
    ],
    rust_extensions=[
        RustExtension(
            "gseapy.gse",
            "Cargo.toml",
            debug="DEBUG" in os.environ,
            binding=Binding.PyO3,
        )
    ],
    entry_points={
        "console_scripts": ["gseapy = gseapy.__main__:main"],
    },
    tests_require=["pytest"],
    cmdclass={"test": PyTest, "sdist": CargoModifiedSdist},
    zip_safe=False,  # Rust extensions are not zip safe
    download_url="https://github.com/zqfang/gseapy",
)